GO annotation for zebrafish
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5 weeks ago
aranyak111 • 0

The first few lines of a mouse genome gene annotation file look like this with both Ensembl gene id and GEO annotation. using Biomart.

Gene stable ID  GO term accession
ENSMUSG00000064372  
ENSMUSG00000064371  
ENSMUSG00000064370  GO:0009055
ENSMUSG00000064370  GO:0016020
ENSMUSG00000064370  GO:0016491
ENSMUSG00000064370  GO:0006122
ENSMUSG00000064370  GO:0008121
ENSMUSG00000064370  GO:0022904
ENSMUSG00000064370  GO:0045275
ENSMUSG00000064370  GO:0016021
ENSMUSG00000064370  GO:0046872
ENSMUSG00000064370  GO:0055114
ENSMUSG00000064370  GO:0005739
ENSMUSG00000064370  GO:0005743
ENSMUSG00000064370  GO:0070469
ENSMUSG00000064370  GO:0031305
ENSMUSG00000064370  GO:0001666
ENSMUSG00000064370  GO:0007584
ENSMUSG00000064370  GO:0009408
ENSMUSG00000064370  GO:0009636
ENSMUSG00000064370  GO:0009725
ENSMUSG00000064370  GO:0010243
ENSMUSG00000064370  GO:0014070
ENSMUSG00000064370  GO:0031100
ENSMUSG00000064370  GO:0033590

. I want to create a similar file for zebrafish genome with Ensembl id and Go annotation. How to go about it?

RNA-Seq • 174 views
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aranyak111 : Please validate answers (green check mark) /comments for your past threads and one such as this. Upvoting/accepting answers is perfect way to show appreciation for volunteers who answer your questions on this site.

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5 weeks ago
GenoMax 99k
  1. Go to Zebrafish Ensembl web page (LINK)
  2. Click on BioMart link at top.
  3. Select Ensembl Genes
  4. Select Zebrafish GRCz11
  5. Under Attributes select External and then under GO --> GO Term accession.
  6. Hit Count button in top left corner. Should be 37241 genes as of today
  7. Click on Results to get the results preview. Should see something like below

Gene stable ID  Gene stable ID version  Transcript stable ID    Transcript stable ID version    GO term accession
ENSDARG00000063344  ENSDARG00000063344.8    ENSDART00000131829  ENSDART00000131829.2    GO:0016020
ENSDARG00000063344  ENSDARG00000063344.8    ENSDART00000131829  ENSDART00000131829.2    GO:0016021
ENSDARG00000063344  ENSDARG00000063344.8    ENSDART00000144883  ENSDART00000144883.3    GO:0016020

  • Choose Export all results to File (default is tab separated values). Be sure to click Unique results only to get unique results. Click Go. Save file.
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Thanks for the feedback. I have been able to obtain GO annotations for the zebrafish I was looking for.

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